The design of the experiments (table with parameters) can be found here. But here is a brief description.

PS N_GENES_INITIAL BITING_RATE_MEAN N_LOCI N_ALLELES_INITIAL
01 120 0.1 2 12
02 1200 0.2 2 120
03 12000 0.5 2 1200

I kept daily biting rates fixed to 1.

1. Basic variables for each scenario across regimes

1.1 diversity

In the complete neutrality, the number of circulating strains seems just too much. This is orders of magnitude more than the selection.

Selection

## [1] "PS: 04 | Scenario: S | exp: 001 | run: 1"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 1"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 1"
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## [1] "PS: 04 | Scenario: S | exp: 001 | run: 4"
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## [1] "PS: 04 | Scenario: S | exp: 001 | run: 5"
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## [1] "PS: 04 | Scenario: S | exp: 001 | run: 7"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 7"
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## [1] "PS: 04 | Scenario: S | exp: 001 | run: 8"
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## [1] "PS: 06 | Scenario: S | exp: 001 | run: 9"
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## [1] "PS: 05 | Scenario: S | exp: 001 | run: 10"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 10"

Complete neutrality

## [1] "PS: 04 | Scenario: N | exp: 001 | run: 1"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 1"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 1"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 2"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 2"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 2"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 3"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 3"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 3"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 4"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 4"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 4"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 5"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 5"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 5"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 6"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 6"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 6"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 7"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 7"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 7"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 8"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 8"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 8"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 9"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 9"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 9"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 10"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 10"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 10"

Generalized immunity

## [1] "PS: 04 | Scenario: G | exp: 001 | run: 1"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 1"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 1"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 2"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 2"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 2"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 3"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 3"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 3"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 4"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 4"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 4"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 5"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 5"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 5"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 6"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 6"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 6"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 7"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 7"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 7"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 8"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 8"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 8"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 9"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 9"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 9"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 10"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 10"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 10"

1.2 EIR

The EIR for selection seems too low? For neutrality it is an order of magnitude more.

Selection

Complete neutrality

Generalized immunity

2. Compare scenarios for a given regime

Notice the order of magnitude difference in the number of repertoires

Low diversity & transmission

## [1] "Scenario: S | exp: 001 | run: 1"
## [1] "Scenario: N | exp: 001 | run: 1"
## [1] "Scenario: G | exp: 001 | run: 1"
## [1] "Scenario: S | exp: 001 | run: 2"
## [1] "Scenario: N | exp: 001 | run: 2"
## [1] "Scenario: G | exp: 001 | run: 2"
## [1] "Scenario: S | exp: 001 | run: 3"
## [1] "Scenario: N | exp: 001 | run: 3"
## [1] "Scenario: G | exp: 001 | run: 3"
## [1] "Scenario: S | exp: 001 | run: 4"
## [1] "Scenario: N | exp: 001 | run: 4"
## [1] "Scenario: G | exp: 001 | run: 4"
## [1] "Scenario: S | exp: 001 | run: 5"
## [1] "Scenario: N | exp: 001 | run: 5"
## [1] "Scenario: G | exp: 001 | run: 5"
## [1] "Scenario: S | exp: 001 | run: 6"
## [1] "Scenario: N | exp: 001 | run: 6"
## [1] "Scenario: G | exp: 001 | run: 6"
## [1] "Scenario: S | exp: 001 | run: 7"
## [1] "Scenario: N | exp: 001 | run: 7"
## [1] "Scenario: G | exp: 001 | run: 7"
## [1] "Scenario: S | exp: 001 | run: 8"
## [1] "Scenario: N | exp: 001 | run: 8"
## [1] "Scenario: G | exp: 001 | run: 8"
## [1] "Scenario: S | exp: 001 | run: 9"
## [1] "Scenario: N | exp: 001 | run: 9"
## [1] "Scenario: G | exp: 001 | run: 9"
## [1] "Scenario: S | exp: 001 | run: 10"
## [1] "Scenario: N | exp: 001 | run: 10"
## [1] "Scenario: G | exp: 001 | run: 10"

Medium diversity & transmission

## [1] "Scenario: S | exp: 001 | run: 1"
## [1] "Scenario: N | exp: 001 | run: 1"
## [1] "Scenario: G | exp: 001 | run: 1"
## [1] "Scenario: S | exp: 001 | run: 2"
## [1] "Scenario: N | exp: 001 | run: 2"
## [1] "Scenario: G | exp: 001 | run: 2"
## [1] "Scenario: S | exp: 001 | run: 3"
## [1] "Scenario: N | exp: 001 | run: 3"
## [1] "Scenario: G | exp: 001 | run: 3"
## [1] "Scenario: S | exp: 001 | run: 4"
## [1] "Scenario: N | exp: 001 | run: 4"
## [1] "Scenario: G | exp: 001 | run: 4"
## [1] "Scenario: S | exp: 001 | run: 5"
## [1] "Scenario: N | exp: 001 | run: 5"
## [1] "Scenario: G | exp: 001 | run: 5"
## [1] "Scenario: S | exp: 001 | run: 6"
## [1] "Scenario: N | exp: 001 | run: 6"
## [1] "Scenario: G | exp: 001 | run: 6"
## [1] "Scenario: S | exp: 001 | run: 7"
## [1] "Scenario: N | exp: 001 | run: 7"
## [1] "Scenario: G | exp: 001 | run: 7"
## [1] "Scenario: S | exp: 001 | run: 8"
## [1] "Scenario: N | exp: 001 | run: 8"
## [1] "Scenario: G | exp: 001 | run: 8"
## [1] "Scenario: S | exp: 001 | run: 9"
## [1] "Scenario: N | exp: 001 | run: 9"
## [1] "Scenario: G | exp: 001 | run: 9"
## [1] "Scenario: S | exp: 001 | run: 10"
## [1] "Scenario: N | exp: 001 | run: 10"
## [1] "Scenario: G | exp: 001 | run: 10"

High diversity & transmission

## [1] "Scenario: S | exp: 001 | run: 1"
## [1] "Scenario: N | exp: 001 | run: 1"
## [1] "Scenario: G | exp: 001 | run: 1"
## [1] "Scenario: S | exp: 001 | run: 2"
## [1] "Scenario: N | exp: 001 | run: 2"
## [1] "Scenario: G | exp: 001 | run: 2"
## [1] "Scenario: S | exp: 001 | run: 3"
## [1] "Scenario: N | exp: 001 | run: 3"
## [1] "Scenario: G | exp: 001 | run: 3"
## [1] "Scenario: S | exp: 001 | run: 4"
## [1] "Scenario: N | exp: 001 | run: 4"
## [1] "Scenario: G | exp: 001 | run: 4"
## [1] "Scenario: S | exp: 001 | run: 5"
## [1] "Scenario: N | exp: 001 | run: 5"
## [1] "Scenario: G | exp: 001 | run: 5"
## [1] "Scenario: S | exp: 001 | run: 6"
## [1] "Scenario: N | exp: 001 | run: 6"
## [1] "Scenario: G | exp: 001 | run: 6"
## [1] "Scenario: S | exp: 001 | run: 7"
## [1] "Scenario: N | exp: 001 | run: 7"
## [1] "Scenario: G | exp: 001 | run: 7"
## [1] "Scenario: S | exp: 001 | run: 8"
## [1] "Scenario: N | exp: 001 | run: 8"
## [1] "Scenario: G | exp: 001 | run: 8"
## [1] "Scenario: S | exp: 001 | run: 9"
## [1] "Scenario: N | exp: 001 | run: 9"
## [1] "Scenario: G | exp: 001 | run: 9"
## [1] "Scenario: S | exp: 001 | run: 10"
## [1] "Scenario: N | exp: 001 | run: 10"
## [1] "Scenario: G | exp: 001 | run: 10"

3. Edge weight values

Selection

Complete Neutrality

Generalized immunity

4. Cutoff (SELECTION)

Cutoff is based on the selection case, so we will look at it more closely. Then we will compare the behavior of the system across scenarios at different cutoffs.

Examples for modules

Persistence and relative persistence

Persistence (months)

Relative persistence

Modules per layer

Repertoires in a module

5. Cutoff – scenario comparison

Examples for modules

Persistence and relative persistence

Module persistence

Persistence (months) Relative persistence

Repertoire persistence

Persistence (months)

Relative persistence

Modules per layer

Repertoires in a module